X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=53642b530103bcb9c4ec61fd704da87481857cf8;hb=d645ed1944459b6271dea2a8511a1e0f4f997530;hp=094628b527e16da67534b08a151c012e1421f7e7;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 094628b..53642b5 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -1,26 +1,32 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-public class DBRefEntry
+import jalview.api.DBRefEntryI;
+
+public class DBRefEntry implements DBRefEntryI
{
String source = "", version = "", accessionId = "";
+ private int startRes, endRes;
/**
* maps from associated sequence to the database sequence's coordinate system
*/
@@ -31,6 +37,7 @@ public class DBRefEntry
}
+
public DBRefEntry(String source, String version, String accessionId)
{
this(source, version, accessionId, null);
@@ -57,21 +64,30 @@ public class DBRefEntry
this.map = map;
}
- public DBRefEntry(DBRefEntry entry)
+ public DBRefEntry(DBRefEntryI entry)
{
- this(
- (entry.source == null ? "" : new String(entry.source)),
- (entry.version == null ? "" : new String(entry.version)),
- (entry.accessionId == null ? "" : new String(entry.accessionId)),
- (entry.map == null ? null : new Mapping(entry.map)));
+ this((entry.getSource() == null ? "" : new String(entry.getSource())),
+ (entry.getVersion() == null ? "" : new String(
+ entry.getVersion())),
+ (entry.getAccessionId() == null ? "" : new String(
+ entry.getAccessionId())),
+ (entry.getMap() == null ? null : new Mapping(entry.getMap())));
}
- public boolean equals(DBRefEntry entry)
+ @Override
+ public boolean equals(Object o)
{
+ // TODO should also override hashCode to ensure equal objects have equal
+ // hashcodes
+ if (o == null || !(o instanceof DBRefEntry))
+ {
+ return false;
+ }
+ DBRefEntry entry = (DBRefEntry) o;
if (entry == this)
+ {
return true;
- if (entry == null)
- return false;
+ }
if (equalRef(entry)
&& ((map == null && entry.map == null) || (map != null
&& entry.map != null && map.equals(entry.map))))
@@ -87,71 +103,71 @@ public class DBRefEntry
* @param entry
* @return true if source, accession and version are equal with those of entry
*/
- public boolean equalRef(DBRefEntry entry)
+ @Override
+ public boolean equalRef(DBRefEntryI entry)
{
if (entry == null)
{
return false;
}
if (entry == this)
+ {
return true;
- if ((source != null && entry.source != null && source
- .equalsIgnoreCase(entry.source))
- && (accessionId != null && entry.accessionId != null && accessionId
- .equalsIgnoreCase(entry.accessionId))
- && (version != null && entry.version != null && version
- .equalsIgnoreCase(entry.version)))
+ }
+ if (entry != null
+ && (source != null && entry.getSource() != null && source
+ .equalsIgnoreCase(entry.getSource()))
+ && (accessionId != null && entry.getAccessionId() != null && accessionId
+ .equalsIgnoreCase(entry.getAccessionId()))
+ && (version != null && entry.getVersion() != null && version
+ .equalsIgnoreCase(entry.getVersion())))
{
return true;
}
return false;
}
+ @Override
public String getSource()
{
return source;
}
+ @Override
public String getVersion()
{
return version;
}
+ @Override
public String getAccessionId()
{
return accessionId;
}
- /**
- * @param accessionId
- * the accessionId to set
- */
+
+ @Override
public void setAccessionId(String accessionId)
{
this.accessionId = accessionId;
}
- /**
- * @param source
- * the source to set
- */
+
+ @Override
public void setSource(String source)
{
this.source = source;
}
- /**
- * @param version
- * the version to set
- */
+
+ @Override
public void setVersion(String version)
{
this.version = version;
}
- /**
- * @return the map
- */
+
+ @Override
public Mapping getMap()
{
return map;
@@ -180,4 +196,34 @@ public class DBRefEntry
return ((source != null) ? source : "") + ":"
+ ((accessionId != null) ? accessionId : "");
}
+
+ @Override
+ public String toString()
+ {
+ return getSrcAccString();
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ @Override
+ public void setStartRes(int startRes)
+ {
+ this.startRes = startRes;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ @Override
+ public void setEndRes(int endRes)
+ {
+ this.endRes = endRes;
+ }
}